We have identified three highly polymorphic microsatellite (simple sequence repeat = SORE) loci, characterized the number of alleles (7-14) and estimate frequencies of these alleles in rhesus macaques of Chinese and Indian origin. For this purpose a non-radioactive method for resolving PCR amplification products on a short polyacrylamide gel and identifying alleles by estimating fragment size (numbers of base pairs) was developed. Parallel analyses of nine electrophoretically defined protein coding loci (polymorphic in rhesus macaques) were conducted on samples drawn from the same (~140) macaques to assess accuracy of earlier estimates of gene diversity. Average heterozygosity based on the sore loci was more than twice that based on protein coding loci; this will allow more accurate future estimates of paternity (and maternity), inbreeding coefficients and changes in genetic heterogeneity of captive colonies. This progress will improve our efforts to study population processes that influence colony productivity because the success of paternity exclusion, required to reconstruct patrilineal relationships in groups of rhesus macaques, highly correlates with the level of heterozygosity of genetic polymorphisms used for paternity exclusion. One such process is loss of fitness due to inbreeding depression in populations with insufficient gene flow. Our recent study of fertility, mortality and rate of weight gain (employed as a measure of physiological efficiency) in inbred and non-inbred rhesus macaques (identified using genetic markers discussed above) revealed no evidence of inbreeding d expression (loss of fitness) at levels of consanguineous inbreeding approximately equal to half-sib mating (f=0.125), A level at which significant loss of fitness occurs in some captive bred species, including some other species of genus macaca. The practical implications of this for colony management are obvious. One theoretical implication this is that selection might not favor male dispersal (in free-ranging groups) solely to avoid inbreeding depression.